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Dinçtürk E. Determination of Raman spectrum under different culture conditions: preliminary research on bacterial fish pathogens. Anim Biotechnol 2024; 35:2299733. [PMID: 38166494 DOI: 10.1080/10495398.2023.2299733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The intensive labour and time required for conventional methods to identify bacterial fish pathogens have revealed the need to develop alternative methods. Raman spectroscopy has been used in the rapid optical identification of bacterial pathogens in recent years as an alternative method in microbiology. Strains of bacterial fish pathogens (Vibrio anguillarum, Lactococcus garvieae and Yersinia ruckeri) that often cause infectious diseases in fish were here identified and analyzed in terms of their biochemical structures in different media and at different incubation times, and the data were specified by using Raman spectroscopy. The results demonstrated that Raman spectroscopy presents species-specific Raman spectra of each disease-causing bacteria and that it would be more appropriate to choose general microbiological media over selective media for routine studies. Additionally, it was found that species-specific band regions did not differ in 24- and 48-hour cultures, but there could be a difference in peak intensity which may lead to difficult characterization of spectrum. The current study, conducted for the first time with bacterial fish pathogens under different incubation conditions, is believed to provide a basis for the routine use of Raman spectroscopy for quick pathogen identification and the precise determination of the methodology for further research.
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Affiliation(s)
- Ezgi Dinçtürk
- Fish Disease and Biotechnology Laboratory, Department of Aquaculture, Izmir Katip Celebi University, Izmir, Türkiye
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2
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Alotaibi G. Prevalence, pandemic, preventions and policies to overcome antimicrobial resistance. Saudi J Biol Sci 2024; 31:104032. [PMID: 38854892 PMCID: PMC11157277 DOI: 10.1016/j.sjbs.2024.104032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/22/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024] Open
Abstract
Antimicrobial resistance (AMR) is a growing concern in Asia, and it is essential to understand the prevalence, pandemic, prevention, and policies to overcome it. According to the World Health Organization (WHO), AMR is one of the main causes of death; in 2019, it was linked to 4.95 million fatalities and caused about 1.27 million deaths. A core package of actions has been provided by WHO to help countries prioritize their needs when creating, carrying out, and overseeing national action plans on antimicrobial resistance. Using a people-cantered approach to AMR, the interventions address the needs and obstacles that individuals and patients encounter when trying to obtain healthcare. The people-cantered core package of AMR treatments seeks to improve public and policymakers; awareness and comprehension of AMR by changing the narrative of AMR to emphasize the needs of people and systemic impairments. Additionally, it backs a more comprehensive and programmatic national response to AMR, which emphasizes the value of fair and inexpensive access to high-quality healthcare services for the avoidance, identification, and management of drug-resistant diseases. The report signals increasing resistance to antibiotics in bacterial infections in humans and the need for better data. In conclusion, the prevalence of AMR in Asia is a significant public health concern, and it is crucial to implement policies and interventions to overcome it.
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Affiliation(s)
- Ghallab Alotaibi
- Department of Pharmacology, College of Pharmacy, Shaqra University, Riyadh 11961, Saudi Arabia
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3
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Shelef O, Kopp T, Tannous R, Arutkin M, Jospe-Kaufman M, Reuveni S, Shabat D, Fridman M. Enzymatic Activity Profiling Using an Ultrasensitive Array of Chemiluminescent Probes for Bacterial Classification and Characterization. J Am Chem Soc 2024; 146:5263-5273. [PMID: 38362863 PMCID: PMC10910560 DOI: 10.1021/jacs.3c11790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
Identification and characterization of bacterial species in clinical and industrial settings necessitate the use of diverse, labor-intensive, and time-consuming protocols as well as the utilization of expensive and high-maintenance equipment. Furthermore, while cutting-edge identification technologies such as mass spectrometry and PCR are highly effective in identifying bacterial pathogens, they fall short in providing additional information for identifying bacteria not present in the databases upon which these methods rely. In response to these challenges, we present a robust and general approach to bacterial identification based on their unique enzymatic activity profiles. This method delivers results within 90 min, utilizing an array of highly sensitive and enzyme-selective chemiluminescent probes. Leveraging our recently developed technology of chemiluminescent luminophores, which emit light under physiological conditions, we have crafted an array of probes designed to rapidly detect various bacterial enzymatic activities. The array includes probes for detecting resistance to the important and large class of β-lactam antibiotics. The analysis of chemiluminescent fingerprints from a diverse range of prominent bacterial pathogens unveiled distinct enzymatic activity profiles for each strain. The reported universally applicable identification procedure offers a highly sensitive and expeditious means to delineate bacterial enzymatic activity fingerprints. This opens new avenues for characterizing and identifying pathogens in research, clinical, and industrial applications.
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Affiliation(s)
| | | | | | - Maxence Arutkin
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moriah Jospe-Kaufman
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Shlomi Reuveni
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Doron Shabat
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond
& Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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4
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Guo Z, Zuo A, Liu X, Jiang Y, Yang S, Lu D. Multiple pulmonary cavities in an immunocompetent patient: a case report and literature review. Front Med (Lausanne) 2024; 11:1329381. [PMID: 38476447 PMCID: PMC10930033 DOI: 10.3389/fmed.2024.1329381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
Legionella pneumonia (LP) is a relatively uncommon yet well-known type of atypical community-acquired pneumonia (CAP). It is characterized by a rapid progression to severe pneumonia and can be easily misdiagnosed. In most patients, chest computed tomography (CT) showed patchy infiltration, which may progress to lobar infiltration or even lobar consolidation. While pulmonary cavities are commonly observed in immunocompromised patients with LP, they are considered rare in immunocompetent individuals. Herein, we present a case of LP in an immunocompetent patient with multiple cavities in both lungs. Pathogen detection was performed using metagenomic next-generation sequencing (mNGS). This case highlights the unusual radiographic presentation of LP in an immunocompetent patient and emphasizes the importance of considering LP as a possible diagnosis in patients with pulmonary cavities, regardless of their immune status. Furthermore, the timely utilization of mNGS is crucial for early pathogen identification, as it provides multiple benefits in enhancing the diagnosis and prognosis of LP patients.
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Affiliation(s)
| | | | | | | | | | - Degan Lu
- Department of Respiratory, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Shandong Institute of Respiratory Diseases, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
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5
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Trigueiro G, Oliveira C, Rodrigues A, Seabra S, Pinto R, Bala Y, Gutiérrez Granado M, Vallejo S, Gonzalez V, Cardoso C. Conversion of a classical microbiology laboratory to a total automation laboratory enhanced by the application of lean principles. Microbiol Spectr 2024; 12:e0215323. [PMID: 38230933 PMCID: PMC10846136 DOI: 10.1128/spectrum.02153-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/03/2023] [Indexed: 01/18/2024] Open
Abstract
Laboratory automation in microbiology improves productivity and reduces sample turnaround times (TATs). However, its full potential can be unlocked through the optimization of workflows by adopting lean principles. This study aimed to explore the relative impact of laboratory automation and continuous improvement events (CIEs) on productivity and TATs. Laboratory automation took place in November 2020 and consisted of the introduction of WASPLab and VITEK MS systems. CIEs were run in May and September 2021. Before the conversion, the laboratory processed about ~492 samples on weekdays and had 10 full-time equivalent (FTE) staff for a productivity of 49 samples/FTE/day. In March 2021, after laboratory automation, the caseload went up to ~621 while the FTEs decreased to 8.5, accounting for productivity improvement to 73 samples/FTE/day. The hypothetical productivity went up to 110 samples/FTE/day following CIEs, meaning that the laboratory could at that point deal with a caseload increase to ~935 with unchanged FTEs. Laboratory conversion also led to an improvement in TATs for all sample types. For vaginal swabs and urine samples, median TATs decreased from 70.3 h [interquartile range (IQR): 63.5-93.1] and 73.7 h (IQR: 35.6-50.7) to 48.2 h (IQR: 44.8-67.7) and 40.0 h (IQR: 35.6-50.7), respectively. Automation alone was responsible for 37.2% and 75.8% of TAT reduction, respectively, while the remaining reduction of 62.8% and 24.2%, respectively, was achieved due to CIEs. The laboratory reached productivity and TAT goals predefined by the management after CIEs. In conclusion, automation substantially improved productivity and TATs, while the subsequent implementation of lean management further unlocked the potential of laboratory automation.IMPORTANCEIn this study, we combined total laboratory automation with lean management to show that appropriate laboratory work organization enhanced the benefit of the automation and substantially contributed to productivity improvements. Globally, the rapid availability of accurate results in the setting of a clinical microbiology laboratory is part of patient-centered approaches to treat infections and helps the implementation of antibiotic stewardship programs backed by the World Health Organization. Locally, from the point of view of laboratory management, it is important to find ways of maximizing the benefits of the use of technology, as total laboratory automation is an expensive investment.
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Affiliation(s)
- Graça Trigueiro
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Carlos Oliveira
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Alexandra Rodrigues
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Sofia Seabra
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Rui Pinto
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
| | - Yohann Bala
- Global Medical Affairs, bioMérieux, Marcy L’Etoile, France
| | | | - Sandra Vallejo
- Lab Consultancy, bioMérieux, bioMérieux SA, Lisbon, Portugal
| | | | - Carlos Cardoso
- Department of Microbiology, Dr. Joaquim Chaves Clinical Analysis Laboratory, Lisbon, Portugal
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Baker KR, Flentie K, Spears BR, Mozharov S, Roberts K, El ganbour A, Somers M, Calkwood J, Liu J, DaPonte K, Sam N, Kaur G, Chen F, Donato J, Chao A, Lewis A, Sherman J, Mortimer K, Harrington AT, Traczewski M, Carpenter D, Shortridge D, Lindley J, Diep A, Norton E, Green M, Gajewski J, Landrith R, Nalubega F, McCallum J, Beiswenger M, Dolan B, Brennan K, Carpenter A, Vacic A, Flyer AN, Pierce VM, Hooper DC, Lewis II JS, Stern E. Multicenter evaluation of the Selux Next-Generation Phenotyping antimicrobial susceptibility testing system. J Clin Microbiol 2024; 62:e0054623. [PMID: 38051069 PMCID: PMC10793272 DOI: 10.1128/jcm.00546-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/12/2023] [Indexed: 12/07/2023] Open
Abstract
The Selux Next-Generation Phenotyping (NGP) system (Charlestown, MA) is a new antimicrobial susceptibility testing system that utilizes two sequential assays performed on all wells of doubling dilution series to determine MICs. A multicenter evaluation of the performance of the Selux NGP system compared with reference broth microdilution was conducted following FDA recommendations and using FDA-defined breakpoints. A total of 2,488 clinical and challenge isolates were included; gram-negative isolates were tested against 24 antimicrobials, and gram-positive isolates were tested against 15 antimicrobials. Data is provided for all organism-antimicrobial combinations evaluated, including those that did and did not meet FDA performance requirements. Overall very major error and major error rates were less than 1% (31/3,805 and 107/15,606, respectively), essential agreement and categorical agreement were >95%, reproducibility was ≥95%, and the average time-to-result (from time of assay start to time of MIC result) was 5.65 hours.
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Affiliation(s)
| | | | | | | | | | | | - Mark Somers
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Jamie Liu
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Nikitha Sam
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Gurleen Kaur
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Felicia Chen
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Alan Chao
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Autumn Lewis
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | | | - Amanda T. Harrington
- Pathology and Laboratory Medicine, Loyola University Medical Center, Maywood, Illinois, USA
| | | | | | | | - Jill Lindley
- JMI Laboratories/Element, North Liberty, Iowa, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Virginia M. Pierce
- Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - David C. Hooper
- Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James S. Lewis II
- Department of Pharmacy Services, Oregon Health and Science University Hospitals and Clinics, Portland, Oregon, USA
| | - Eric Stern
- Selux Diagnostics, Charlestown, Massachusetts, USA
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Migliorisi G, Calvo M, Collura A, Di Bernardo F, Perez M, Scalia G, Stefani S. The Rapid Phenotypic Susceptibility Testing in Real-Life Experience: How the MIC Values Impact on Sepsis Fast Diagnostic Workflow. Diagnostics (Basel) 2023; 14:56. [PMID: 38201365 PMCID: PMC10802849 DOI: 10.3390/diagnostics14010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
The MIC value definition faithfully reflects antimicrobial sensitivity, profoundly impacting the infection's clinical outcome. Our study aimed to evaluate the Accelerate PhenoTM System in defining the importance of fast phenotypic susceptibility data. A number of 270 monomicrobial samples simultaneously underwent standard procedures and fast protocols after a contemporary Gram stain. Finally, we provided Turn-around Time (TAT) and statistical evaluations. The fast technology required a medium value of 7 h to complete ID and AST profiles. Although there were some spectrum limitations, it revealed an optimal success rate in microbial identification directly from positive blood cultures. The Gram-negative AST reached a 98.9% agreement between the Accelerate Pheno™ System and the standard method. In addition, the Gram-positive AST gathered a 98.7% agreement comparing the same systems. The chance to rapidly provide precise MIC values is one of the last frontiers in clinical microbiology, especially in high-prevalence antimicrobial resistance areas.
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Affiliation(s)
- Giuseppe Migliorisi
- U.O.C. Laboratory Analysis A.O.U. “Policlinico—San Marco”, Via Santa Sofia 78, 95123 Catania, Italy; (M.C.); (S.S.)
| | - Maddalena Calvo
- U.O.C. Laboratory Analysis A.O.U. “Policlinico—San Marco”, Via Santa Sofia 78, 95123 Catania, Italy; (M.C.); (S.S.)
| | - Antonina Collura
- U.O.C. Clinical Microbiology, “Civico-Di Cristina-Benfratelli” Hospital, Piazza Nicola Leotta 4, 90127 Palermo, Italy
| | - Francesca Di Bernardo
- U.O.C. Clinical Microbiology, “Civico-Di Cristina-Benfratelli” Hospital, Piazza Nicola Leotta 4, 90127 Palermo, Italy
| | - Marianna Perez
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Guido Scalia
- U.O.C. Laboratory Analysis A.O.U. “Policlinico—San Marco”, Via Santa Sofia 78, 95123 Catania, Italy; (M.C.); (S.S.)
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
| | - Stefania Stefani
- U.O.C. Laboratory Analysis A.O.U. “Policlinico—San Marco”, Via Santa Sofia 78, 95123 Catania, Italy; (M.C.); (S.S.)
- Department of Biomedical and Biotechnological Sciences, University of Catania, Via Santa Sofia 97, 95123 Catania, Italy
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Taha AE, Alduraywish AS, Alanazi AA, Alruwaili AH, Alruwaili AL, Alrais MM, Alyousef AA, Alrais AA, Alanazi MA, Alhudaib SN, Alazmi BM. High Bacterial Contamination Load of Self-Service Facilities in Sakaka City, Aljouf, Saudi Arabia, with Reduced Sensitivity to Some Antimicrobials. Microorganisms 2023; 11:2937. [PMID: 38138082 PMCID: PMC10745763 DOI: 10.3390/microorganisms11122937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/01/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Although self-service facilities (SSFs) have been used on a large scale worldwide, they can be easily contaminated by microorganisms from the hands of their sequential users. This research aimed to study the prevalence and antimicrobial susceptibility/resistance of bacteria contaminating SSFs in Sakaka, Aljouf, Saudi Arabia. We randomly swabbed the surfaces of 200 SSFs, then used the suitable culture media, standard microbiological methods, and the MicroScan WalkAway Microbiology System, including the identification/antimicrobial susceptibility testing-combo panels. A high SSFs' bacterial contamination load was detected (78.00%). Ninety percent of the samples collected in the afternoon, during the maximum workload of the SSFs, yielded bacterial growth (p < 0.001 *). Most of the contaminated SSFs were supermarket payment machines, self-pumping equipment at gas stations (p = 0.004 *), online banking service machines (p = 0.026 *), and barcode scanners in supermarkets. In the antiseptic-deficient areas, 55.1% of the contaminated SSFs were detected (p = 0.008 *). Fifty percent of the contaminated SSFs were not decontaminated. The most common bacterial contaminants were Escherichia coli (70 isolates), Klebsiella pneumoniae (66 isolates), Staphylococcus epidermidis (34 isolates), methicillin-resistant Staphylococcus aureus (18 isolates), and methicillin-sensitive Staphylococcus aureus (14 isolates), representing 31.53%, 29.73%, 15.32%, 8.11%, and 6.31% of the isolates, respectively. Variable degrees of reduced sensitivity to some antimicrobials were detected among the bacterial isolates. The SSFs represent potential risks for the exchange of antimicrobial-resistant bacteria between the out-hospital environment and the hospitals through the hands of the public. As technology and science advance, there is an urgent need to deploy creative and automated techniques for decontaminating SSFs and make use of recent advancements in materials science for producing antibacterial surfaces.
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Affiliation(s)
- Ahmed E. Taha
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
| | | | - Ali A. Alanazi
- College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
| | | | | | - Mmdoh M. Alrais
- College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
| | | | | | | | | | - Bandar M. Alazmi
- College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia
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9
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Mohamed EI, Turkey MS, Meshref RA, Ghazal AA, Shawky SM, Aboulela AG. Electronic nose versus VITEK 2 system for the rapid diagnosis of bloodstream infections. Braz J Microbiol 2023; 54:2857-2865. [PMID: 37872278 PMCID: PMC10689606 DOI: 10.1007/s42770-023-01154-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
Infectious diseases that spread through the bloodstream, known as bloodstream infections (BSIs), are a major global health problem. Positive outcomes for patients with sepsis are typically the result of prompt treatment started after an early diagnosis of BSIs. In this study, we evaluated the capabilities of a portable electronic nose (E-Nose) to detect BSIs with two commonly isolated Gram-negative bacterial species, E. coli and K. pneumonia. One hundred and five blood samples were randomly collected for blood culture examinations using BACTEC and VITEK 2 system, and headspace analysis by an E-Nose from June to December 2021. Classification accuracy of E. coli, K. pneumonia, and negative controls was measured using principal component analysis, area under the receiver operating characteristic curve, sensitivity, and specificity analysis. After incubation for 24 h, cluster plots generated using principal component analysis demonstrated that E-Nose could accurately diagnose the presence of E. coli and K. pneumonia in BACTEC blood culture bottles with a sensitivity and specificity of 100% in just 120 s. The E-Nose method has been shown to be an immediate, precise, and cost-effective alternative to automated blood culture BACTEC and VITEK 2 systems for the fast detection of the causative bacterial pathogens of BSIs in clinical practice. Thus, patients with such Gram-negative bacteremia can have guided empirical antimicrobial therapy on the same day of BSIs diagnosis, which can be lifesaving.
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Affiliation(s)
- Ehab I Mohamed
- Medical Biophysics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt.
| | - Mohamed S Turkey
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
- Microbiology and Immunology Department, Faculty of Pharmacy, October 6 University, Sixth of October City, Giza, Egypt
| | - Radwa A Meshref
- Medical Equipment Technology Department, Faculty of Applied Health Sciences Technology, Pharos University, Alexandria, Egypt
| | - Abeer A Ghazal
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Sherine M Shawky
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Aliaa G Aboulela
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
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10
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Khadse SN, Ugemuge S, Singh C. Impact of Antimicrobial Stewardship on Reducing Antimicrobial Resistance. Cureus 2023; 15:e49935. [PMID: 38179391 PMCID: PMC10765068 DOI: 10.7759/cureus.49935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Antimicrobial resistance has become a serious global issue, posing a significant threat to public health and healthcare professionals. Since the advent of penicillin, many antibiotics have lost their effectiveness in combating microbes simply due to inappropriate, irrational, unnecessary, and unrestricted use. The ineffectiveness of an increasing number of antibiotics necessitates the utilization of more potent antimicrobial agents for combatting uncomplicated infections. In response to the escalating prevalence of multidrug-resistant pathogens and the imperative to curtail the demand for novel antibiotics, the Antimicrobial Stewardship Program was conceived and implemented. This initiative is characterized by a lead physician, ideally possessing expertise in infectious diseases, alongside a pharmacist serving as a secondary leader and a microbiologist with defined responsibilities to achieve several objectives. These objectives include reducing indiscriminate usage of antimicrobial agents, promoting selective antimicrobial utilization based on culture results, de-escalating therapy from broad-spectrum to targeted antimicrobial agents, and transitioning from parenteral to oral administration when feasible. These objectives are pursued through a combination of pre-prescription and post-prescription strategies. While the Antimicrobial Stewardship Program is widely established in developed nations, a pressing need exists for its more comprehensive implementation in less developed regions. This review aims to examine the strategies used in antimicrobial stewardship programs to evaluate their effectiveness in preventing the development of multidrug-resistant organisms (MDROs) based on existing research studies. Under the Antimicrobial Stewardship Program, education of healthcare professionals and continuous disposal of information about antimicrobial resistance have helped to restrict the emergence of multidrug-resistant organisms.
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Affiliation(s)
- Sagar N Khadse
- Medical Education, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research, Nagpur, IND
| | - Sarita Ugemuge
- Microbiology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research, Nagpur, IND
| | - Charu Singh
- Microbiology, Datta Meghe Medical College, Datta Meghe Institute of Higher Education and Research, Nagpur, IND
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11
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Strubbe G, Messiaen AS, Vandendriessche S, Verhasselt B, Boelens J. EUCAST rapid antimicrobial susceptibility testing (RAST) compared to conventional susceptibility testing: implementation and potential added value in a tertiary hospital in Belgium. Acta Clin Belg 2023; 78:385-391. [PMID: 36999562 DOI: 10.1080/17843286.2023.2197314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 03/26/2023] [Indexed: 04/01/2023]
Abstract
OBJECTIVES EUCAST breakpoints for short incubation disk diffusion allow rapid antimicrobial susceptibility testing (RAST) directly from positive blood cultures. We evaluate the RAST methodology and assess its potential added value in a setting of low prevalence of multidrug-resistant (MDR) organisms. METHODS In our two-part study, we performed RAST on 127 clinical blood cultures at 6 and 8 h and determined categorical agreement with direct susceptibility testing. We also measure the impact of susceptibility results on antimicrobial therapy compared to empirical treatment. RESULTS Categorical agreement was 96.2% at 6 h (575/598 isolate-drug combinations) and 96.6% at 8 h (568/588 combinations). Major errors involved piperacillin/tazobactam in 16 of 31 cases. The second part of our study shows that AST reporting proved essential in correcting ineffective empirical therapy in 6.3% of the patients (8/126). CONCLUSION EUCAST RAST is an inexpensive and reliable method of susceptibility testing, although care must be taken with reporting piperacillin/tazobactam. In support of RAST implementation, we show that AST remains of great importance in providing effective therapy, even in a setting of low MDR prevalence and elaborate antibiotic guidelines.
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Affiliation(s)
- Gregory Strubbe
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | | | | | - Bruno Verhasselt
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jerina Boelens
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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12
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Richter-Dahlfors A, Kärkkäinen E, Choong FX. Fluorescent optotracers for bacterial and biofilm detection and diagnostics. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2023; 24:2246867. [PMID: 37680974 PMCID: PMC10481766 DOI: 10.1080/14686996.2023.2246867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/03/2023] [Accepted: 08/07/2023] [Indexed: 09/09/2023]
Abstract
Effective treatment of bacterial infections requires methods that accurately and quickly identify which antibiotic should be prescribed. This review describes recent research on the development of optotracing methodologies for bacterial and biofilm detection and diagnostics. Optotracers are small, chemically well-defined, anionic fluorescent tracer molecules that detect peptide- and carbohydrate-based biopolymers. This class of organic molecules (luminescent conjugated oligothiophenes) show unique electronic, electrochemical and optical properties originating from the conjugated structure of the compounds. The photophysical properties are further improved as donor-acceptor-donor (D-A-D)-type motifs are incorporated in the conjugated backbone. Optotracers bind their biopolymeric target molecules via electrostatic interactions. Binding alters the optical properties of these tracer molecules, shown as altered absorption and emission spectra, as well as ON-like switch of fluorescence. As the optotracer provides a defined spectral signature for each binding partner, a fingerprint is generated that can be used for identification of the target biopolymer. Alongside their use for in situ experimentation, optotracers have demonstrated excellent use in studies of a number of clinically relevant microbial pathogens. These methods will find widespread use across a variety of communities engaged in reducing the effect of antibiotic resistance. This includes basic researchers studying molecular resistance mechanisms, academia and pharma developing new antimicrobials targeting biofilm infections and tests to diagnose biofilm infections, as well as those developing antibiotic susceptibility tests for biofilm infections (biofilm-AST). By iterating between the microbial world and that of plants, development of the optotracing technology has become a prime example of successful cross-feeding across the boundaries of disciplines. As optotracers offers a capacity to redefine the way we work with polysaccharides in the microbial world as well as with plant biomass, the technology is providing novel outputs desperately needed for global impact of the threat of antimicrobial resistance as well as our strive for a circular bioeconomy.
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Affiliation(s)
- Agneta Richter-Dahlfors
- AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Fiber and Polymer Technology, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Elina Kärkkäinen
- AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ferdinand X. Choong
- AIMES – Center for the Advancement of Integrated Medical and Engineering Sciences at Karolinska Institutet and KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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Marutescu LG. Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control. Microorganisms 2023; 11:1300. [PMID: 37317273 DOI: 10.3390/microorganisms11051300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050095 Bucharest, Romania
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14
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Han JY, Yeh M, DeVoe DL. Nanogap traps for passive bacteria concentration and single-point confocal Raman spectroscopy. BIOMICROFLUIDICS 2023; 17:024101. [PMID: 36896354 PMCID: PMC9991444 DOI: 10.1063/5.0142118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
A microfluidic device enabling the isolation and concentration of bacteria for analysis by confocal Raman spectroscopy is presented. The glass-on-silicon device employs a tapered chamber surrounded by a 500 nm gap that serves to concentrate cells at the chamber apex during sample perfusion. The sub-micrometer gap retains bacteria by size exclusion while allowing smaller contaminants to pass unimpeded. Concentrating bacteria within the fixed volume enables the use of single-point confocal Raman detection for the rapid acquisition of spectral signatures for bacteria identification. The technology is evaluated for the analysis of E. cloacae, K. pneumoniae, and C. diphtheriae, with automated peak extraction yielding distinct spectral fingerprints for each pathogen at a concentration of 103 CFU/ml that compare favorably with spectra obtained from significantly higher concentration reference samples evaluated by conventional confocal Raman analysis. The nanogap technology offers a simple, robust, and passive approach to concentrating bacteria from dilute samples into well-defined optical detection volumes, enabling rapid and sensitive confocal Raman detection for label-free identification of focused cells.
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Affiliation(s)
| | - Michael Yeh
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Don L. DeVoe
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
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15
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Salam MA, Al-Amin MY, Pawar JS, Akhter N, Lucy IB. Conventional methods and future trends in antimicrobial susceptibility testing. Saudi J Biol Sci 2023; 30:103582. [PMID: 36852413 PMCID: PMC9958398 DOI: 10.1016/j.sjbs.2023.103582] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/07/2023] [Accepted: 01/29/2023] [Indexed: 02/12/2023] Open
Abstract
Antimicrobial susceptibility testing is an essential task for selecting appropriate antimicrobial agents to treat infectious diseases. Constant evolution has been observed in methods used in the diagnostic microbiology laboratories. Disc diffusion or broth microdilution are classical and conventional phenotypic methods with long turnaround time and labour-intensive but still widely practiced as gold-standard. Scientists are striving to develop innovative, novel and faster methods of antimicrobial susceptibility testing to be applicable for routine microbiological laboratory practice and research. To meet the requirements, there is an increasing trend towards automation, genotypic and micro/nano technology-based innovations. Automation in detection systems and integration of computers for online data analysis and data sharing are giant leaps towards versatile nature of automated methods currently in use. Genotypic methods detect a specific genetic marker associated with resistant phenotypes using molecular amplification techniques and genome sequencing. Microfluidics and microdroplets are recent addition in the continuous advancement of methods that show great promises with regards to safety and speed and have the prospect to identify and monitor resistance mechanisms. Although genotypic and microfluidics methods have many exciting features, however, their applications into routine clinical laboratory practice warrant extensive validation. The main impetus behind the evolution of methods in antimicrobial susceptibility testing is to shorten the overall turnaround time in obtaining the results and to enhance the ease of sample processing. This comprehensive narrative review summarises major conventional phenotypic methods and automated systems currently in use, and highlights principles of some of the emerging genotypic and micro/nanotechnology-based methods in antimicrobial susceptibility testing.
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Key Words
- ADR, Adverse drug reaction
- AMR, Antimicrobial resistance
- AST, Antimicrobial susceptibility testing
- ATCC, American Type Culture Collection
- Advantages and disadvantages
- Antimicrobial susceptibility testing
- Automations
- CFU, Colony forming units
- CLSI, Clinical & Laboratory Standards Institute
- Conventional methods
- DOT-MGA, Direct-On-Target Microdroplet Growth Assay
- EUCAST, European Committee on Antimicrobial Susceptibility Testing
- Etest, Epsilometer testing
- Genotypic methods
- ID, Identification
- MALDI-TOF MS, Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry
- MBC, Minimum bactericidal concentration
- MDR, Multi drug resistant
- MHA, Muller Hinton Agar
- MIC, Minimum inhibitory concentration
- Micro/nanotechnology-based techniques
- NAAT, Nucleic Acid Amplification Test
- PCR, Polymerase chain reaction
- PMF, Peptide mass fingerprint
- POC, Point of care
- WGS, Whole Genome Sequencing
- ZOI, Zone of inhibition
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Affiliation(s)
- Md. Abdus Salam
- Department of Basic Medical Sciences, Kulliyyah of Medicine, International Islamic University, Malaysia
| | - Md. Yusuf Al-Amin
- Purdue University Interdisciplinary Life Sciences Graduate Program, Purdue University, West Lafayette, IN, USA,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Jogendra Singh Pawar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Naseem Akhter
- Department of Neurology, Henry Ford Health System, Detroit, MI 48202, USA
| | - Irine Banu Lucy
- Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh,Corresponding author at: Department of Physics, University of Rajshahi, Rajshahi 6205, Bangladesh.
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Peterson SW, Demczuk W, Martin I, Adam H, Bharat A, Mulvey MR. Identification of bacterial and fungal pathogens directly from clinical blood cultures using whole genome sequencing. Genomics 2023; 115:110580. [PMID: 36792020 DOI: 10.1016/j.ygeno.2023.110580] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 01/17/2023] [Accepted: 02/11/2023] [Indexed: 02/16/2023]
Abstract
Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.
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Affiliation(s)
- S W Peterson
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - W Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - I Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - H Adam
- Diagnostic Services, Shared Health Manitoba, Health Sciences Centre, Winnipeg, Manitoba, Canada
| | - A Bharat
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
| | - M R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
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Zakaria ND, Hamzah HH, Salih IL, Balakrishnan V, Abdul Razak K. A Review of Detection Methods for Vancomycin-Resistant Enterococci (VRE) Genes: From Conventional Approaches to Potentially Electrochemical DNA Biosensors. BIOSENSORS 2023; 13:294. [PMID: 36832060 PMCID: PMC9954664 DOI: 10.3390/bios13020294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Vancomycin-resistant Enterococci (VRE) genes are bacteria strains generated from Gram-positive bacteria and resistant to one of the glycopeptides antibiotics, commonly, vancomycin. VRE genes have been identified worldwide and exhibit considerable phenotypic and genotypic variations. There are six identified phenotypes of vancomycin-resistant genes: VanA, VanB, VanC, VanD, VanE, and VanG. The VanA and VanB strains are often found in the clinical laboratory because they are very resistant to vancomycin. VanA bacteria can pose significant issues for hospitalized patients due to their ability to spread to other Gram-positive infections, which changes their genetic material to increase their resistance to the antibiotics used during treatment. This review summarizes the established methods for detecting VRE strains utilizing traditional, immunoassay, and molecular approaches and then focuses on potential electrochemical DNA biosensors to be developed. However, from the literature search, no information was reported on developing electrochemical biosensors for detecting VRE genes; only the electrochemical detection of vancomycin-susceptible bacteria was reported. Thus, strategies to create robust, selective, and miniaturized electrochemical DNA biosensor platforms to detect VRE genes are also discussed.
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Affiliation(s)
- Nor Dyana Zakaria
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Hairul Hisham Hamzah
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Ibrahim Luqman Salih
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Venugopal Balakrishnan
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
| | - Khairunisak Abdul Razak
- Nanobiotechnology Research and Innovation (NanoBRI), Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor 11800, Penang, Malaysia
- School of Materials and Mineral Resources Engineering, Universiti Sains Malaysia, Nibong Tebal 14300, Penang, Malaysia
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18
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Hernàndez-Carnerero À, Sànchez-Marrè M, Mora-Jiménez I, Soguero-Ruiz C, Martínez-Agüero S, Álvarez-Rodríguez J. Dimensionality reduction and ensemble of LSTMs for antimicrobial resistance prediction. Artif Intell Med 2023; 138:102508. [PMID: 36990585 DOI: 10.1016/j.artmed.2023.102508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 11/21/2022] [Accepted: 02/04/2023] [Indexed: 02/10/2023]
Abstract
Bacterial resistance to antibiotics has been rapidly increasing, resulting in low antibiotic effectiveness even treating common infections. The presence of resistant pathogens in environments such as a hospital Intensive Care Unit (ICU) exacerbates the critical admission-acquired infections. This work focuses on the prediction of antibiotic resistance in Pseudomonas aeruginosa nosocomial infections at the ICU, using Long Short-Term Memory (LSTM) artificial neural networks as the predictive method. The analyzed data were extracted from the Electronic Health Records (EHR) of patients admitted to the University Hospital of Fuenlabrada from 2004 to 2019 and were modeled as Multivariate Time Series. A data-driven dimensionality reduction method is built by adapting three feature importance techniques from the literature to the considered data and proposing an algorithm for selecting the most appropriate number of features. This is done using LSTM sequential capabilities so that the temporal aspect of features is taken into account. Furthermore, an ensemble of LSTMs is used to reduce the variance in performance. Our results indicate that the patient's admission information, the antibiotics administered during the ICU stay, and the previous antimicrobial resistance are the most important risk factors. Compared to other conventional dimensionality reduction schemes, our approach is able to improve performance while reducing the number of features for most of the experiments. In essence, the proposed framework achieve, in a computationally cost-efficient manner, promising results for supporting decisions in this clinical task, characterized by high dimensionality, data scarcity, and concept drift.
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19
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Shim H. Three Innovations of Next-Generation Antibiotics: Evolvability, Specificity, and Non-Immunogenicity. Antibiotics (Basel) 2023; 12:antibiotics12020204. [PMID: 36830114 PMCID: PMC9952447 DOI: 10.3390/antibiotics12020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Antimicrobial resistance is a silent pandemic exacerbated by the uncontrolled use of antibiotics. Since the discovery of penicillin, we have been largely dependent on microbe-derived small molecules to treat bacterial infections. However, the golden era of antibiotics is coming to an end, as the emergence and spread of antimicrobial resistance against these antibacterial compounds are outpacing the discovery and development of new antibiotics. The current antibiotic market suffers from various shortcomings, including the absence of profitability and investment. The most important underlying issue of traditional antibiotics arises from the inherent properties of these small molecules being mostly broad-spectrum and non-programmable. As the scientific knowledge of microbes progresses, the scientific community is starting to explore entirely novel approaches to tackling antimicrobial resistance. One of the most prominent approaches is to develop next-generation antibiotics. In this review, we discuss three innovations of next-generation antibiotics compared to traditional antibiotics as specificity, evolvability, and non-immunogenicity. We present a number of potential antimicrobial agents, including bacteriophage-based therapy, CRISPR-Cas-based antimicrobials, and microbiome-derived antimicrobial agents. These alternative antimicrobial agents possess innovative properties that may overcome the inherent shortcomings of traditional antibiotics, and some of these next-generation antibiotics are not merely far-fetched ideas but are currently in clinical development. We further discuss some related issues and challenges such as infection diagnostics and regulatory frameworks that still need to be addressed to bring these next-generation antibiotics to the antibiotic market as viable products to combat antimicrobial resistance using a diversified set of strategies.
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Affiliation(s)
- Hyunjin Shim
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea
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20
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Pérez Jorge G, Rodrigues dos Santos Goes IC, Gontijo MTP. Les misérables: a Parallel Between Antimicrobial Resistance and COVID-19 in Underdeveloped and Developing Countries. Curr Infect Dis Rep 2022; 24:175-186. [PMID: 36211535 PMCID: PMC9531231 DOI: 10.1007/s11908-022-00788-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 12/02/2022]
Abstract
Purpose of Review The COVID-19 pandemic has been responsible for more than 6.3 million deaths worldwide. During the pandemic, the indiscriminate use of antibiotics has increased, contributing to the spread of multidrug-resistant bacteria. In this review, we aim to determine the spread and impact of antibiotic treatments in patients with COVID-19, focusing on underdeveloped and developing countries. Recent Findings Meta-analysis revealed that bacterial co-infections and secondary infections are relatively rare in COVID-19 patients, corresponding to less than 20% of hospitalized patients. Even so, most of these patients have received antibiotic treatments. Summary This review discusses how the COVID-19 pandemic could increase the emergence of multidrug-resistant strains to currently available antibiotics. Initially, we discussed the spread and impact of multidrug resistance of ESKAPE pathogens associated with nosocomial infections and analyzed their risk of secondary infections in patients with COVID-19. Then we highlight three factors related to the spread of resistant bacteria during the current pandemic: overprescription of antibiotics followed by self-medication. Finally, we discussed the lack of availability of diagnostic tests to discriminate the etiologic agent of a disease. All these factors lead to inappropriate use of antibiotics and, therefore, to an increase in the prevalence of resistance, which can have devastating consequences shortly. The data compiled in this study underscore the importance of epidemiological surveillance of hospital isolates to provide new strategies for preventing and controlling infections caused by multidrug-resistant bacteria. In addition, the bibliographic research also highlights the need for an improvement in antibiotic prescribing in the health system.
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Affiliation(s)
- Genesy Pérez Jorge
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP 13083-862 Brazil
- Laboratorio de Investigaciones Biomédicas, Universidad de Sucre, Cra. 28 #5-267, Sincelejo, Sucre, Colômbia
| | - Isabella Carolina Rodrigues dos Santos Goes
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP 13083-862 Brazil
| | - Marco Tulio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP 13083-862 Brazil
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 10 Duke Medicine Cir, Durham, NC 27710 USA
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Lakhan C, Badrie N, Ramsubhag A, Indar L. Detection of Foodborne Pathogens in Acute Gastroenteritis Patient’s Stool Samples Using the BioFire® FilmArray® Gastrointestinal PCR Panel in the Republic of Trinidad and Tobago, West Indies. Microorganisms 2022; 10:microorganisms10081601. [PMID: 36014019 PMCID: PMC9416176 DOI: 10.3390/microorganisms10081601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
In 2009, the burden of illness study for acute gastroenteritis in Trinidad and Tobago highlighted that ~10% of stool samples tested were positive for a foodborne pathogen. The study also noted that limited laboratory screening for pathogens contributed to a lack of etiology as public health hospitals only routinely tested for Salmonella and Shigella, and sometimes for Escherichia coli and Campylobacter. To better understand the foodborne pathogens responsible for acute gastroenteritis, enhanced testing using the BioFire® FilmArray® Gastrointestinal PCR panel was used to screen diarrheal stool samples for 22 pathogens from patients in 2018. The five general public health hospitals (San Fernando, Mt. Hope, Port of Spain, Sangre Grande, and Tobago) were notified of research activities and diarrheal stool samples were collected from all acute gastroenteritis patients. A total of 66 stools were screened and ~30% of samples tested positive for a foodborne pathogen. The current study showed that a much wider range of enteric pathogens were associated with acute gastroenteritis in Trinidad and Tobago than previously reported in 2009. These findings can be used by health officials to guide appropriate interventions, as well as to provide evidence for adoption of the PCR panel detection method at public health hospitals to benefit patient care.
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Affiliation(s)
- Carelene Lakhan
- Department of Food Production, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Neela Badrie
- Department of Food Production, University of the West Indies, St. Augustine, Trinidad and Tobago
- Correspondence: ; Tel.: +1868-662-2002 (ext. 83211); Fax: +1868-663-9684
| | - Adash Ramsubhag
- Department of Life Sciences, University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Lisa Indar
- The Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
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22
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Ota Y, Okada R, Takahashi H, Saito R. Molecular detection of fluoroquinolone-resistant Neisseria meningitidis by using mismatched PCR-restriction fragment length polymorphism technique. Front Cell Infect Microbiol 2022; 12:911911. [PMID: 35982783 PMCID: PMC9378782 DOI: 10.3389/fcimb.2022.911911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Ciprofloxacin (CIP) is a commonly used antibiotic for meningococcal chemoprophylaxis, and the mutations in the quinolone resistance-determining region of gyrA are associated with CIP-resistant Neisseria meningitidis. Here, we established a mismatched PCR-restriction fragment length polymorphism (RFLP) assay to detect a mutation at codon 91 of gyrA, followed by high-level CIP-resistant meningococci. We designed PCR-RFLP primers to detect the T91I mutation in gyrA by introducing an artificial AciI cleavage site. This assay was performed using 26 N. meningitidis strains whose gyrA sequences have been characterized. The amplified 160 bp PCR product from gyrA was digested into three fragments (80, 66, and 14 bp) when there was no mutation, or two fragments (146 and 14 bp) when there was a mutation at codon 91. A correlation was observed between the mismatched PCR-RFLP assay and gyrA sequencing. This rapid, simple, and accurate assay has the potential to detect CIP-resistant N. meningitidis in clinical microbiology laboratories, contributing to the appropriate antibiotic selection for meningococcal chemoprophylaxis, will help maintain an effective treatment for close contacts of IMD patients, and prevent the spread of CIP-resistant N. meningitidis.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Reina Okada
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Ryoichi Saito,
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A side-by-side comparison of the performance and time-and-motion data of VITEK MS. Eur J Clin Microbiol Infect Dis 2022; 41:1115-1125. [PMID: 35841452 DOI: 10.1007/s10096-022-04472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2022]
Abstract
Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry systems are designed for rapid and reliable microbial identification. VITEK MS PRIME is the bioMérieux's new generation instrument equipped with a continuous load-and-go sample loading system, urgent slide prioritization for critical patient samples and new internal components for faster identification. The aim of this study was to assess the performance of VITEK MS PRIME and to compare it to that of the VITEK MS system. In addition, at two sites, we performed a time-and-motion study to evaluate the efficiency of sample analysis from colony picking to slide removal from the instrument. We analyzed by VITEK MS and VITEK MS PRIME a total of 1413 isolates (1320 bacterial and 76 yeast) deriving from routine diagnostic samples that came into four laboratories in Canada, France, Italy, and Spain. VITEK MS PRIME and VITEK MS were concordant to the species and genus level for 1354/1413 (95.8%) and to the species level for 1341/1413 (94.9%). The identification and concordance rates in individual centers were largely homogenous. Overall, VITEK MS PRIME identified 1370/1413 (97.0%) of isolates compared to 1367/1413 (96.7%) identified by VITEK MS. Identification rates were consistently high for all microorganism categories. A time-and-motion study showed that the use of VITEK MS PRIME was associated with significant time saving. VITEK MS PRIME performs as well as VITEK MS and reduces the time necessary for pathogen identification. To fully optimize the laboratory process and obtain maximum efficiency, VITEK MS PRIME must be integrated into the laboratory workflow.
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24
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Omi M, Matsuo Y, Araki-Sasaki K, Oba S, Yamada H, Hirota K, Takahashi K. 16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study. BMJ Open Ophthalmol 2022; 7:bmjophth-2021-000910. [PMID: 36161861 PMCID: PMC9131114 DOI: 10.1136/bmjophth-2021-000910] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Objective We conducted a feasibility study to verify the effectiveness of 16S ribosomal RNA (rRNA) gene analysis using the nanopore sequencer MinION for identifying causative bacteria in several types of ocular infections. Methods and Analysis Four cases of corneal ulcers, one case of endophthalmitis and one case of a conjunctival abscess were included in this study. DNA was extracted from corneal scraping, vitreous samples and secretions from the conjunctival abscess. We conducted 16S rRNA gene amplicon sequencing using MinION and metagenomic DNA analysis. The efficacy of bacterial identification was verified by comparing the conventional culture method with smear observations. Results 16S rRNA gene sequencing analysis with MinION identified the causative organisms promptly with high accuracy in approximately 4 hours, from ophthalmic specimens. The results of the conventional culture method and 16S rRNA gene sequencing were consistent in all cases. In four of the six cases, a greater variety of organisms was found in the 16S rRNA gene analysis than in bacterial culture. Conclusion Using our workflow, 16S rRNA gene analysis using MinION enabled rapid and accurate identification possible in various kinds of bacterial ocular infections.
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Affiliation(s)
- Masatoshi Omi
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Kansai Medical University, Hirakata, Japan
| | | | - Shimpei Oba
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Haruhiko Yamada
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Kansai Medical University, Hirakata, Japan
| | - Kanji Takahashi
- Department of Ophthalmology, Kansai Medical University, Hirakata, Japan
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Metabolic preference assay for rapid diagnosis of bloodstream infections. Nat Commun 2022; 13:2332. [PMID: 35484129 PMCID: PMC9050716 DOI: 10.1038/s41467-022-30048-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/14/2022] [Indexed: 12/13/2022] Open
Abstract
Bloodstream infections (BSIs) cause >500,000 infections and >80,000 deaths per year in North America. The length of time between the onset of symptoms and administration of appropriate antimicrobials is directly linked to mortality rates. It currently takes 2–5 days to identify BSI pathogens and measure their susceptibility to antimicrobials – a timeline that directly contributes to preventable deaths. To address this, we demonstrate a rapid metabolic preference assay (MPA) that uses the pattern of metabolic fluxes observed in ex-vivo microbial cultures to identify common pathogens and determine their antimicrobial susceptibility profiles. In a head-to-head race with a leading platform (VITEK 2, BioMérieux) used in diagnostic laboratories, MPA decreases testing timelines from 40 hours to under 20. If put into practice, this assay could reduce septic shock mortality and reduce the use of broad spectrum antibiotics. It is currently slow to identify bloodstream infection pathogens. Here the authors report a rapid metabolic preference assay that uses the pattern of metabolic fluxes observed in ex-vivo microbial cultures to identify common pathogens and determine their antimicrobial susceptibility profiles.
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Antimicrobial Susceptibility Testing: A Comprehensive Review of Currently Used Methods. Antibiotics (Basel) 2022; 11:antibiotics11040427. [PMID: 35453179 PMCID: PMC9024665 DOI: 10.3390/antibiotics11040427] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Antimicrobial resistance (AMR) has emerged as a major threat to public health globally. Accurate and rapid detection of resistance to antimicrobial drugs, and subsequent appropriate antimicrobial treatment, combined with antimicrobial stewardship, are essential for controlling the emergence and spread of AMR. This article reviews common antimicrobial susceptibility testing (AST) methods and relevant issues concerning the advantages and disadvantages of each method. Although accurate, classic technologies used in clinical microbiology to profile antimicrobial susceptibility are time-consuming and relatively expensive. As a result, physicians often prescribe empirical antimicrobial therapies and broad-spectrum antibiotics. Although recently developed AST systems have shown advantages over traditional methods in terms of testing speed and the potential for providing a deeper insight into resistance mechanisms, extensive validation is required to translate these methodologies to clinical practice. With a continuous increase in antimicrobial resistance, additional efforts are needed to develop innovative, rapid, accurate, and portable diagnostic tools for AST. The wide implementation of novel devices would enable the identification of the optimal treatment approaches and the surveillance of antibiotic resistance in health, agriculture, and the environment, allowing monitoring and better tackling the emergence of AMR.
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Qu X, Wang S, Qu Y, Wang H, Ye X, Tang L, Xie Q. Antimicrobial Susceptibility Characteristics and Risk Factors Associated with Adult Sepsis in Wenzhou, China. Infect Drug Resist 2022; 15:915-924. [PMID: 35299859 PMCID: PMC8921831 DOI: 10.2147/idr.s352570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 02/25/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To clarify the distribution of pathogenic bacteria by analyzing the bacterial susceptibility characteristics and risk factors for adult sepsis in The Wenzhou city, Zhejiang province, China, and to aid early diagnosis, monitoring, and prognosis prediction in cases of bacterial sepsis. Patients and Methods We retrospectively analyzed 329 patients with sepsis admitted to the Second Affiliated Hospital of Wenzhou Medical University between January 2018 and March 2021. Laboratory data were collected before and after treatment; moreover, the bacterial susceptibility characteristics and risk factors for sepsis were comprehensively analyzed using the Sequential Organ Failure Assessment (SOFA) score. Results The SOFA score was negatively correlated with the prognosis (P < 0.05). We isolated 47 pathogenic strains from blood culture samples, including 29 gram-positive strains, 18 gram-negative strains. The most common gram-negative pathogens in blood cultures are Klebsiella pneumoniae and Escherichia coli, while the most common gram-positive pathogens are Staphylococcus aureus and Staphylococcus hominis. Gram-negative pathogens had resistance rates of 77% and 62.5% to ciprofloxacin and ceftriaxone, respectively. Gram-positive bacteria had a high resistance to penicillin at 100%. Prognostic factors for sepsis included patients’ consciousness, SOFA score, prothrombin time, international normalized ratio, fibrinogen, D-dimer, and aspartate aminotransferase (P < 0.05). Of these, the D-dimer level could predict the outcome of patients with sepsis (AUC = 0.661, P < 0.05). Conclusion The pathogens detected in adult sepsis in Wenzhou are mainly Klebsiella pneumoniae, Escherichia coli, Staphylococcus aureus, and Staphylococcus hominis. The pathogens exhibited differences in drug susceptibility. The optimal antibiotics should be chosen based on the principles of rational use and drug susceptibility. Combined with D-dimer levels, these parameters can be used to determine the optimal strategy for preventing and treating pathogenic bacteria.
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Affiliation(s)
- Xiaoxiao Qu
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, People’s Republic of China
| | - Shishi Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, People’s Republic of China
| | - Ying Qu
- Department of Clinical Laboratory, Wenzhou People’s Hospital, The Third Affiliated Hospital of Shanghai University, The Third Clinical Institute Affiliated to Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Huiyan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, People’s Republic of China
| | - Xuanmei Ye
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, People’s Republic of China
| | - Luming Tang
- Emergency Department, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, People’s Republic of China
| | - Qipeng Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, People’s Republic of China
- Correspondence: Qipeng Xie, Department of Clinical Laboratory, The Second Affiliated Hospital & Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China, Tel +86 151 577 87159, Email
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Xu J, Yi X, Jin G, Peng D, Fan G, Xu X, Chen X, Yin H, Cooper JM, Huang WE. High-Speed Diagnosis of Bacterial Pathogens at the Single Cell Level by Raman Microspectroscopy with Machine Learning Filters and Denoising Autoencoders. ACS Chem Biol 2022; 17:376-385. [PMID: 35026119 DOI: 10.1021/acschembio.1c00834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate and rapid identification of infectious bacteria is important in medicine. Raman microspectroscopy holds great promise in performing label-free identification at the single-cell level. However, due to the naturally weak Raman signal, it is a challenge to build extensive databases and achieve both accurate and fast identification. Here, we used signal-to-noise ratio (SNR) as a standard indicator for Raman data quality and performed bacterial identification using 11, 141 single-cell Raman spectra from nine bacterial strains. Subsequently, using two machine learning methods, a simple filter, and a neural network-based denoising autoencoder (DAE), we demonstrated 92% (simple filter using 1 s/cell spectra) and 84% (DAE using 0.1 s/cell spectra) identification accuracy. Our machine learning-aided Raman analysis paves the way for high-speed Raman microspectroscopic clinical diagnostics.
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Affiliation(s)
- Jiabao Xu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
| | - Xiaofei Yi
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Guilan Jin
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Di Peng
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Gaoya Fan
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Huabing Yin
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Jonathan M. Cooper
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
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Aslam B, Khurshid M, Arshad MI, Muzammil S, Rasool M, Yasmeen N, Shah T, Chaudhry TH, Rasool MH, Shahid A, Xueshan X, Baloch Z. Antibiotic Resistance: One Health One World Outlook. Front Cell Infect Microbiol 2021; 11:771510. [PMID: 34900756 PMCID: PMC8656695 DOI: 10.3389/fcimb.2021.771510] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance (ABR) is a growing public health concern worldwide, and it is now regarded as a critical One Health issue. One Health’s interconnected domains contribute to the emergence, evolution, and spread of antibiotic-resistant microorganisms on a local and global scale, which is a significant risk factor for global health. The persistence and spread of resistant microbial species, and the association of determinants at the human-animal-environment interface can alter microbial genomes, resulting in resistant superbugs in various niches. ABR is motivated by a well-established link between three domains: human, animal, and environmental health. As a result, addressing ABR through the One Health approach makes sense. Several countries have implemented national action plans based on the One Health approach to combat antibiotic-resistant microbes, following the Tripartite’s Commitment Food and Agriculture Organization (FAO)-World Organization for Animal Health (OIE)-World Health Organization (WHO) guidelines. The ABR has been identified as a global health concern, and efforts are being made to mitigate this global health threat. To summarize, global interdisciplinary and unified approaches based on One Health principles are required to limit the ABR dissemination cycle, raise awareness and education about antibiotic use, and promote policy, advocacy, and antimicrobial stewardship.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Maria Rasool
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nafeesa Yasmeen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Tamoor Hamid Chaudhry
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan.,Public Health Laboratories Division, National Institute of Health, Islamabad, Pakistan
| | | | - Aqsa Shahid
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Xia Xueshan
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
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Ito CAS, Bail L, Arend LNVS, Silva KO, Michelotto SS, Nogueira KDS, Tuon FF. Evaluation of MicroScan WalkAway for Determination of Ceftazidime-Avibactam and Ceftolozane-Tazobactam Susceptibility in Carbapenem-Resistant Gram-Negative Bacilli. J Clin Microbiol 2021; 59:e0153621. [PMID: 34586889 PMCID: PMC8601251 DOI: 10.1128/jcm.01536-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/24/2021] [Indexed: 12/27/2022] Open
Abstract
We evaluated the performance of ceftazidime-avibactam and ceftolozane-tazobactam MicroScan Neg multidrug-resistant MIC 1 (NMR1) panel for clinical carbapenem-nonsusceptible Gram-negative bacilli isolates. We evaluated 212 clinically significant carbapenem-nonsusceptible Gram-negative bacilli (139 Pseudomonas aeruginosa and 73 KPC-producing Enterobacterales) from 71 Brazilian hospitals (2013 to 2020). Ceftazidime-avibactam and ceftolozane-tazobactam MICs from the panel were compared with a broth microdilution (BMD) test as the reference method. Essential agreement (EA) and categorical agreement (CA) were assessed. For P. aeruginosa, antimicrobial susceptibility testing error rates were calculated using the error-rate bound method. Discrepancies were initially observed with 11 isolates; 4 resolved after retesting, 2 in favor of the NMR1 and 2 in favor of the BMD method. The ceftazidime-avibactam EA (overall and evaluable) was 100% for P. aeruginosa and Enterobacterales. The CA was 100% for Enterobacterales and 98.6% for P. aeruginosa. The ceftolozane-tazobactam EA was 98.6% and 100% (overall and evaluable, respectively), and the CA was 96.4% for P. aeruginosa. For ceftazidime/avibactam, no very major error (VME) was found, and the major error (ME) rate was 4.2% (2/48). For ceftolozane-tazobactam and P. aeruginosa, using the CLSI breakpoints, the minor error (mE) was 11.4%, and no VME or ME was found. While using EUCAST breakpoints, the VME was 11.4% with no ME. The mE becomes ME or VME in the absence of the intermediate category. All categorical errors were also within 1 log of MIC variation, and the adjusted error rate for CLSI/EUCAST was 0% (0/212). The NMR1 panel is an option to test ceftazidime-avibactam for KPC-producing Enterobacterales and carbapenem-nonsusceptible P. aeruginosa. When a MIC of 4 mg/liter for ceftolozane-tazobactam is obtained using this method, an alert could be created, and the results could be confirmed by an alternative method.
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Affiliation(s)
- Carmen Antonia Sanches Ito
- Division of Microbiology, Universidade Estadual de Ponta Grossa do Paraná, Ponta Grossa, Paraná, Brazil
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Larissa Bail
- Division of Microbiology, Universidade Estadual de Ponta Grossa do Paraná, Ponta Grossa, Paraná, Brazil
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Lavinia Nery Villa Stangler Arend
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
- Laboratório Central do Estado do Paraná–LACEN, Curitiba, Paraná, Brazil
| | | | | | - Keite da Silva Nogueira
- Hospital de Clínicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Basic Pathology Department, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
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Nanayakkara AK, Boucher HW, Fowler VG, Jezek A, Outterson K, Greenberg DE. Antibiotic resistance in the patient with cancer: Escalating challenges and paths forward. CA Cancer J Clin 2021; 71:488-504. [PMID: 34546590 DOI: 10.3322/caac.21697] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/13/2022] Open
Abstract
Infection is the second leading cause of death in patients with cancer. Loss of efficacy in antibiotics due to antibiotic resistance in bacteria is an urgent threat against the continuing success of cancer therapy. In this review, the authors focus on recent updates on the impact of antibiotic resistance in the cancer setting, particularly on the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.). This review highlights the health and financial impact of antibiotic resistance in patients with cancer. Furthermore, the authors recommend measures to control the emergence of antibiotic resistance, highlighting the risk factors associated with cancer care. A lack of data in the etiology of infections, specifically in oncology patients in United States, is identified as a concern, and the authors advocate for a centralized and specialized surveillance system for patients with cancer to predict and prevent the emergence of antibiotic resistance. Finding better ways to predict, prevent, and treat antibiotic-resistant infections will have a major positive impact on the care of those with cancer.
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Affiliation(s)
- Amila K Nanayakkara
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
| | - Helen W Boucher
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Boston, Massachusetts
| | - Vance G Fowler
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Amanda Jezek
- Infectious Diseases Society of America, Arlington, Virginia
| | - Kevin Outterson
- CARB-X, Boston, Massachusetts
- Boston University School of Law, Boston, Massachusetts
| | - David E Greenberg
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, University of Texas Southwestern, Dallas, Texas
- Department of Microbiology, University of Texas Southwestern, Dallas, Texas
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Arreguin-Campos R, Eersels K, Lowdon JW, Rogosic R, Heidt B, Caldara M, Jiménez-Monroy KL, Diliën H, Cleij TJ, van Grinsven B. Biomimetic sensing of Escherichia coli at the solid-liquid interface: From surface-imprinted polymer synthesis toward real sample sensing in food safety. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106554] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Sophian A, Purwaningsih R, Muindar M, Igirisa EPJ, Amirullah ML. Detection of Salmonella typhimurium ATCC 14028 in Powder Prepared Traditional Medicines Using Real-Time PCR. BORNEO JOURNAL OF PHARMACY 2021. [DOI: 10.33084/bjop.v4i3.1838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The detection of Salmonella typhimurium ATCC 14028 using real-time PCR on powdered traditional medicinal products was carried out in the microbiology and molecular biology testing laboratory of the Food and Drug Administration in Gorontalo. This research aims to provide a reference for alternative testing methods in testing the products of traditional powder preparations on the market. The sample consisted of 10 traditional powder preparations spiked with positive control of S. typhimurium ATCC 14028 phase 2. The method used in the study was real-time PCR analysis using the SYBR® Green method, while DNA isolation using the direct PCR method. Data analysis was performed by analyzing the sample's melting temperature (Tm) curve and comparing it with positive control. The results showed that S. typhimurium ATCC 14028 was detected in samples at an average Tm value of 84.18°C, with ranges of 84.0-84.5°C. For positive control, the Tm value was at 85.2°C, while for the negative control, the Tm value was not detected. Based on these data, it can be concluded that S. typhimurium ATCC 14028 in traditional medicine products powder preparations can be detected using real-time PCR.
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Affiliation(s)
- Alfi Sophian
- National Agency of Drug and Food Control of Republic of Indonesia
| | | | - Muindar Muindar
- National Agency of Drug and Food Control of Republic of Indonesia in Gorontalo
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Anton-Vazquez V, Hine P, Krishna S, Chaplin M, Planche T. Rapid versus standard antimicrobial susceptibility testing to guide treatment of bloodstream infection. Cochrane Database Syst Rev 2021; 5:CD013235. [PMID: 34097767 PMCID: PMC8561756 DOI: 10.1002/14651858.cd013235.pub2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
BACKGROUND Rapid antimicrobial susceptibility tests are expected to reduce the time to clinically important results of a blood culture. This might enable clinicians to better target therapy to a person's needs, and thereby, improve health outcomes (mortality, length of hospital stay), and reduce unnecessary prescribing of broad-spectrum antibiotics; thereby reducing antimicrobial resistance rates. OBJECTIVES To assess the effects of rapid susceptibility testing versus standard susceptibility testing for bloodstream infections (BSIs). SEARCH METHODS To identify studies with selected outcomes, we searched the Cochrane Infectious Diseases Group Specialised Register, CENTRAL, MEDLINE, LILACS, and two trials registries, between 1987 and October 2020. We used 'bloodstream infection' and 'antimicrobial susceptibility tests' as search terms. We had no language or publication status limitations. SELECTION CRITERIA Randomized controlled trials (RCTs) comparing rapid antimicrobial susceptibility testing (with a time-to-result of ≤ 8 hours) versus conventional antimicrobial susceptibility testing in people with a BSI caused by any bacteria, as identified by a positive blood culture. DATA COLLECTION AND ANALYSIS Two review authors independently screened references, full-text reports of potentially relevant studies, extracted data from the studies, and assessed risk of bias. Any disagreement was discussed and resolved with a third review author. For mortality, a dichotomous outcome, we extracted the number of events in each arm, and presented a risk ratio (RR) with 95% confidence interval (CI) to compare rapid susceptibility testing to conventional methods. We used Review Manager 5.4 to meta-analyse the data. For other outcomes, which are time-to-event outcomes (time-to-discharge from hospital, time-to-first appropriate antibiotic change), we conducted qualitative narrative synthesis, due to heterogeneity of outcome measures. MAIN RESULTS: We included six trials, with 1638 participants. For rapid antimicrobial susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.10, 95% CI 0.82 to 1.46; 6 RCTs, 1638 participants; low-certainty evidence). In subgroup analysis, for rapid genotypic or molecular antimicrobial susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.02, 95% CI 0.69 to 1.49; 4 RCTs, 1074 participants; low-certainty evidence). For phenotypic rapid susceptibility testing compared to conventional methods, there was little or no difference in mortality between groups (RR 1.37, 95% CI 0.80 to 2.35; 2 RCTs, 564 participants; low-certainty evidence). In qualitative analysis, rapid susceptibility testing may make little or no difference in time-to-discharge (4 RCTs, 1165 participants; low-certainty evidence). In qualitative analysis, rapid genotypic susceptibility testing compared to conventional testing may make little or no difference in time-to-appropriate antibiotic (3 RCTs, 929 participants; low-certainty evidence). In subgroup analysis, rapid phenotypic susceptibility testing compared to conventional testing may improve time-to-appropriate antibiotic (RR -17.29, CI -45.05 to 10.47; 2 RCTs, 564 participants; low-certainty evidence). AUTHORS' CONCLUSIONS: The theoretical benefits of rapid susceptibility testing have not been demonstrated to directly improve mortality, time-to-discharge, or time-to-appropriate antibiotic in these randomized studies. Future large prospective studies should be designed to focus on the most clinically meaningful outcomes, and aim to optimize blood culture pathways.
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Affiliation(s)
- Vanesa Anton-Vazquez
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - Paul Hine
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sanjeev Krishna
- Institute of Infection and Immunity, St George's University of London, London, UK
| | - Marty Chaplin
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Timothy Planche
- Medical Microbiology Department, SouthWest London Pathology, Jenner Wing St George's Hospital, London, UK
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Evaluation of a New Culture-Based AtbFinder Test-System Employing a Novel Nutrient Medium for the Selection of Optimal Antibiotics for Critically Ill Patients with Polymicrobial Infections within 4 h. Microorganisms 2021; 9:microorganisms9050990. [PMID: 34064335 PMCID: PMC8147811 DOI: 10.3390/microorganisms9050990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/28/2021] [Accepted: 05/02/2021] [Indexed: 11/28/2022] Open
Abstract
Here, we describe the validation of a new phenotypic culture-based AtbFinder method for rapid selection of antibiotics in vitro using specimens with mono- and polybacterial infections. AtbFinder, which can be applied to any type of non-blood tissue, does not require isolation of pure bacterial cultures. The method uses a novel TGV medium that allows more rapid bacterial growth of Gram-positive and Gram-negative monoisolates compared with that achieved with conventional laboratory media, demonstrating overall sensitivity, specificity, PPV, NPV values of 99.6%, 98.1%, 98.5%, and 99.4%, respectively, after 4 h. For polymicrobial infections, AtbFinder utilized a novel paradigm of the population response to antibiotics, enabling bacterial growth in the form of a mixed microbial community and selecting antibiotics targeting not only the principal pathogen, but also those bacteria that support their growth. TGV medium allowed culturing of a more diverse set of bacteria from polymicrobial biospecimens, compared with that achieved with the standard media, and enabled, within 4 h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, the AtbFinder system may be a valuable tool in improving antibiotic selection, and enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients.
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Zhang P, Kaushik AM, Mach KE, Hsieh K, Liao JC, Wang TH. Facile syringe filter-enabled bacteria separation, enrichment, and buffer exchange for clinical isolation-free digital detection and characterization of bacterial pathogens in urine. Analyst 2021; 146:2475-2483. [PMID: 33899069 PMCID: PMC10697054 DOI: 10.1039/d1an00039j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The development of accelerated methods for pathogen identification (ID) and antimicrobial susceptibility testing (AST) for infectious diseases is necessary to facilitate evidence-based antibiotic therapy and reduce clinical overreliance on broad-spectrum antibiotics. Towards this end, droplet-based microfluidics has unlocked remarkably rapid diagnostic assays with single-cell and single-molecule resolution. Yet, droplet platforms invariably rely on testing purified bacterial samples that have been clinically isolated after lengthy (>16 h) plating. While plating-based clinical isolation is important for enriching and separating out bacteria from background in clinical samples and also facilitating buffer exchange, it creates a diagnostic bottleneck that ultimately precludes droplet-based methods from achieving significantly accelerated times-to-result. To alleviate this bottleneck, we have developed facile syringe filter-enabled strategies for bacterial separation, enrichment, and buffer exchange from urine samples. By selecting appropriately sized filter membranes, we separated bacterial cells from background particulates in urine samples and achieved up to 91% bacterial recovery after such 1-step filtration. When interfaced with droplet-based detection of bacterial cells, 1-step filtration improved the limit of detection for bacterial ID and quantification by over an order of magnitude. We also developed a facile buffer exchange strategy to prepare bacteria in urine samples for droplet-based AST that achieved up to 10-fold bacterial enrichment during buffer exchange. Our filtration strategies, can be easily integrated into droplet workflows, enable clinical isolation-free sample-to-answer ID and AST, and significantly accelerate the turnaround of standard infectious disease diagnostic workflows.
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Affiliation(s)
- Pengfei Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.
| | - Aniruddha M Kaushik
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph C Liao
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA. and Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, USA
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Performance evaluation of Alfred 60AST rapid susceptibility testing directly from positive blood cultures in the routine laboratory workflow. Eur J Clin Microbiol Infect Dis 2021; 40:1487-1494. [PMID: 33598828 DOI: 10.1007/s10096-021-04191-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022]
Abstract
The aim of this study was to evaluate the performance of the new automated system Alfred60AST which is based on light scattering technology for rapid susceptibility testing directly from positive blood cultures as well as its applicability in the routine laboratory workflow. We evaluated 176 significant episodes of bacteremia due to 92 Gram-negative and 84 Gram-positive bacteria. The antimicrobial agents tested were ceftriaxone, ciprofloxacin, gentamicin, meropenem, piperacillin-tazobactam, and colistin for Gram negatives and cefoxitin, vancomycin, linezolid, and daptomycin for Gram positives. Concordance assessment was performed in comparison with our routine method, Vitek2 (bioMérieux). Discrepancies were resolved with MICRONAUT-S (Merlin) or E-test (bioMérieux). Out of 690 susceptibility determinations, 94.05% showed categorical agreement (CA) with the routine method and this percentage increased to 94.49 after discrepancy analysis. There were 1.45% very major errors, 3.33% major errors, and 1.16% minor errors (decreased to 1.45, 3.04, and 1.01 after discrepancy analysis). The CA for most of the antibiotics was above 90% except for daptomycin for Gram positives (87.30%) and ceftriaxone for Gram negatives (88.23%). The concordance was slightly better for Gram negative than for Gram-positive bacteria (94.30 versus 93.70%, respectively). The total turnaround time for a complete Alfred60AST result was 6-6.5h. The evaluated method gave rapid and reliable results in a few hours, versus 48h for the conventional one. Implementing this technology in routine workflow allows clinicians to optimize the treatment on the same day of blood culture positivity with potential positive clinical benefits and impact on antibiotic stewardship.
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Low L, Fuentes-Utrilla P, Hodson J, O’Neil JD, Rossiter AE, Begum G, Suleiman K, Murray PI, Wallace GR, Loman NJ, Rauz S. Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis. PeerJ 2021; 9:e10778. [PMID: 33628638 PMCID: PMC7891086 DOI: 10.7717/peerj.10778] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative. Nanopore sequencing technology is portable and capable of generating long sequencing reads in real-time. The aim of this study is to evaluate the potential of nanopore sequencing directly from clinical samples for the diagnosis of bacterial microbial keratitis. METHODS Using full-length 16S rRNA amplicon sequences from a defined mock microbial community, we evaluated and benchmarked our bioinformatics analysis pipeline for taxonomic assignment on three different 16S rRNA databases (NCBI 16S RefSeq, RDP and SILVA) with clustering at 97%, 99% and 100% similarities. Next, we optimised the sample collection using an ex vivo porcine model of microbial keratitis to compare DNA recovery rates of 12 different collection methods: 21-gauge needle, PTFE membrane (4 mm and 6 mm), Isohelix™ SK-2S, Sugi® Eyespear, Cotton, Rayon, Dryswab™, Hydraflock®, Albumin-coated, Purflock®, Purfoam and Polyester swabs. As a proof-of-concept study, we then used the sampling technique that provided the highest DNA recovery, along with the optimised bioinformatics pipeline, to prospectively collected samples from patients with suspected microbial keratitis. The resulting nanopore sequencing results were then compared to standard microbiology culture methods. RESULTS We found that applying alignment filtering to nanopore sequencing reads and aligning to the NCBI 16S RefSeq database at 100% similarity provided the most accurate bacterial taxa assignment. DNA concentration recovery rates differed significantly between the collection methods (p < 0.001), with the Sugi® Eyespear swab providing the highest mean rank of DNA concentration. Then, applying the optimised collection method and bioinformatics pipeline directly to samples from two patients with suspected microbial keratitis, sequencing results from Patient A were in agreement with culture results, whilst Patient B, with negative culture results and previous antibiotic use, showed agreement between nanopore and Illumina Miseq sequencing results. CONCLUSION We have optimised collection methods and demonstrated a novel workflow for identification of bacterial microbial keratitis using full-length 16S nanopore sequencing.
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Affiliation(s)
- Liying Low
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Pablo Fuentes-Utrilla
- MicrobesNG/School of Biosciences, University of Birmingham, Birmingham, West Midlands, UK
| | - James Hodson
- Queen Elizabeth Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, West Midlands, UK
| | - John D. O’Neil
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
| | - Amanda E. Rossiter
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, West Midlands, UK
| | - Ghazala Begum
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Birmingham, UK
| | - Kusy Suleiman
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
| | - Philip I. Murray
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Graham R. Wallace
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
| | - Nicholas J. Loman
- MicrobesNG/School of Biosciences, University of Birmingham, Birmingham, West Midlands, UK
| | - Saaeha Rauz
- Academic Unit of Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, West Midlands, UK
- Birmingham and Midland Eye Centre, Sandwell and West Birmingham Hospitals National Health Service (NHS) Trust, Birmingham, West Midlands, UK
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Robinson ED, Stilwell A, Attai AE, Donohue LE, Shah MD, Hill BK, Elliott ZS, Poulter M, Brewster F, Cox HL, Mathers AJ. Implementation of a Rapid Phenotypic Susceptibility Platform for Gram-Negative Bloodstream Infections with Paired Antimicrobial Stewardship Intervention: Is the Juice Worth the Squeeze? Clin Infect Dis 2021; 73:783-792. [PMID: 33580233 PMCID: PMC8423462 DOI: 10.1093/cid/ciab126] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Implementation of the Accelerate Pheno TM Gram-negative platform (RDT) paired with antimicrobial stewardship program (ASP) intervention projects to improve time to institutional-preferred antimicrobial therapy (IPT) for Gram-negative bacilli (GNB) bloodstream infections (BSI). However, few data describe the impact of discrepant RDT results from standard of care (SOC) methods on antimicrobial prescribing. METHODS A single-center, pre-/post-intervention study of consecutive, non-duplicate blood cultures for adult inpatients with GNB BSI following combined RDT + ASP intervention was performed. The primary outcome was time to IPT. An a priori definition of IPT was utilized to limit bias and allow for an assessment of the impact of discrepant RDT results with the SOC reference standard. RESULTS Five hundred fourteen patients (PRE 264; POST 250) were included. Median time to antimicrobial susceptibility testing (AST) results decreased 29.4 hours (p < 0.001) post-intervention, and median time to IPT was reduced by 21.2 hours (p <0.001). Utilization (days of therapy [DOTs]/1000 days present) of broad-spectrum agents decreased (PRE 655.2 vs. POST 585.8; p = 0.043) and narrow-spectrum beta-lactams increased (69.1 vs 141.7; p <0.001). Discrepant results occurred in 69/250 (28%) post-intervention episodes, resulting in incorrect ASP recommendations in 10/69 (14%). No differences in clinical outcomes were observed. CONCLUSIONS While implementation of a phenotypic RDT + ASP can improve time to IPT, close coordination with Clinical Microbiology and continued ASP follow up are needed to optimize therapy. Although uncommon, the potential for erroneous ASP recommendations to de-escalate to inactive therapy following RDT results warrants further investigation.
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Affiliation(s)
- Evan D Robinson
- Division of Infectious Diseases and International Health. Department of Medicine, University of Virginia Health. Charlottesville, Virginia, USA
| | - Allison Stilwell
- Department of Pharmacy Services, New York-Presbyterian Brooklyn Methodist Hospital, Brooklyn, New York, USA
| | - April E Attai
- Clinical Microbiology Laboratory. Department of Pathology, University of Virginia Health, Charlottesville, Virginia, USA
| | - Lindsay E Donohue
- Department of Pharmacy Services, University of Virginia Health, Charlottesville, Virginia, USA
| | - Megan D Shah
- Department of Pharmacy Services, University of Virginia Health, Charlottesville, Virginia, USA
| | - Brandon K Hill
- Department of Pharmacy Services, University of Virginia Health, Charlottesville, Virginia, USA
| | - Zachary S Elliott
- Department of Pharmacy Services, University of Virginia Health, Charlottesville, Virginia, USA
| | - Melinda Poulter
- Clinical Microbiology Laboratory. Department of Pathology, University of Virginia Health, Charlottesville, Virginia, USA
| | - Frankie Brewster
- Clinical Microbiology Laboratory. Department of Pathology, University of Virginia Health, Charlottesville, Virginia, USA
| | - Heather L Cox
- Division of Infectious Diseases and International Health. Department of Medicine, University of Virginia Health. Charlottesville, Virginia, USA.,Department of Pharmacy Services, University of Virginia Health, Charlottesville, Virginia, USA
| | - Amy J Mathers
- Division of Infectious Diseases and International Health. Department of Medicine, University of Virginia Health. Charlottesville, Virginia, USA.,Clinical Microbiology Laboratory. Department of Pathology, University of Virginia Health, Charlottesville, Virginia, USA
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40
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Wang R, Erickson D. Paper-Based Semi-quantitative Antimicrobial Susceptibility Testing. ACS OMEGA 2021; 6:1410-1414. [PMID: 33490800 PMCID: PMC7818583 DOI: 10.1021/acsomega.0c05060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/18/2020] [Indexed: 05/02/2023]
Abstract
Antimicrobial resistance is increasingly recognized as a major threat to global health. To combat this emerging threat, accessible antimicrobial susceptibility testing should be prioritized as a key component of stewardship efforts. In this work, we developed a user-friendly paper-based test that provides visual readout of bacterial antibiotic susceptibility in a semiquantitative format. We leveraged on-chip paper microfluidics to enable multiplexed testing of multiple antibiotic dilutions with a single sample addition step, replicating the functionality of traditional broth-dilution-based susceptibility testing in a simplified format. Our paper-based test offers several advantages including low sample volume requirement and lack of need for humidity control during incubation, an innovation that addresses a key limitation of conventional paper-microfluidic devices. Using several clinically relevant bacterial organisms and antimicrobial agents, we demonstrate that our colorimetric readout approach provides a strong predictor of susceptibility category.
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Affiliation(s)
- Ruisheng Wang
- Meinig
School of Biomedical Engineering, Cornell
University, Ithaca, New York 14853, United States
| | - David Erickson
- Sibley
School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14853, United States
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41
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Bryan NC, Lebreton F, Gilmore M, Ruvkun G, Zuber MT, Carr CE. Genomic and Functional Characterization of Enterococcus faecalis Isolates Recovered From the International Space Station and Their Potential for Pathogenicity. Front Microbiol 2021; 11:515319. [PMID: 33505359 PMCID: PMC7829349 DOI: 10.3389/fmicb.2020.515319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/09/2020] [Indexed: 01/07/2023] Open
Abstract
Enterococcus faecalis is a multidrug resistant, opportunistic human pathogen and a leading cause of hospital acquired infections. Recently, isolates have been recovered from the air and surfaces onboard the International Space Station (ISS). Pangenomic and functional analyses were carried out to assess their potential impact on astronaut health. Genomes of each ISS isolate, and both clinical and commensal reference strains, were evaluated for their core and unique gene content, acquired antibiotic resistance genes, phage, plasmid content, and virulence traits. In order to determine their potential survival when outside of the human host, isolates were also challenged with three weeks of desiccation at 30% relative humidity. Finally, pathogenicity of the ISS strains was evaluated in the model organism Caenorhabditis elegans. At the culmination of this study, there were no defining signatures that separated known pathogenic strains from the more commensal phenotypes using the currently available resources. As a result, the current reliance on database information alone must be shifted to experimentally evaluated genotypic and phenotypic characteristics of clinically relevant microorganisms.
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Affiliation(s)
- Noelle C Bryan
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Francois Lebreton
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, United States.,Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Michael Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, MA, United States
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States
| | - Maria T Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Christopher E Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, United States.,Georgia Institute of Technology, Atlanta, GA, United States
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Tsang KK, Maguire F, Zubyk HL, Chou S, Edalatmand A, Wright GD, Beiko RG, McArthur AG. Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance. Microb Genom 2021; 7:mgen000500. [PMID: 33416461 PMCID: PMC8115898 DOI: 10.1099/mgen.0.000500] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 12/08/2020] [Indexed: 11/25/2022] Open
Abstract
Diagnosing antimicrobial resistance (AMR) in the clinic is based on empirical evidence and current gold standard laboratory phenotypic methods. Genotypic methods have the potential advantages of being faster and cheaper, and having improved mechanistic resolution over phenotypic methods. We generated and applied rule-based and logistic regression models to predict the AMR phenotype from Escherichia coli and Pseudomonas aeruginosa multidrug-resistant clinical isolate genomes. By inspecting and evaluating these models, we identified previously unknown β-lactamase substrate activities. In total, 22 unknown β-lactamase substrate activities were experimentally validated using targeted gene expression studies. Our results demonstrate that generating and analysing predictive models can help guide researchers to the mechanisms driving resistance and improve annotation of AMR genes and phenotypic prediction, and suggest that we cannot solely rely on curated knowledge to predict resistance phenotypes.
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Affiliation(s)
- Kara K. Tsang
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Finlay Maguire
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haley L. Zubyk
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sommer Chou
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arman Edalatmand
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D. Wright
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Andrew G. McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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Ukuhor HO. The interrelationships between antimicrobial resistance, COVID-19, past, and future pandemics. J Infect Public Health 2021; 14:53-60. [PMID: 33341485 PMCID: PMC7831651 DOI: 10.1016/j.jiph.2020.10.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/21/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 was first reported in Wuhan, China in December 2019 and is associated with high levels of morbidity and mortality. Various types of bacterial and fungal infections occur in patients with COVID-19 with some resistant to antimicrobials that are associated with significantly worse outcomes and deaths. Besides, antimicrobial-resistant (AMR) co-infections are responsible for clinically significant mortality in past pandemics. There is evidence to suggest that factors such as the proliferation of adulterated antimicrobials in some developing countries, international travels, issues with healthcare financing, use/misuse by humans, and in agricultural production and climate change are determinants of AMR at various levels of society. These complex interrelated determinants intersect with AMR in current and past pandemics and could amplify the potential of a future antimicrobial resistance pandemic. Therefore, global concerted interventions targeted at all levels of society to reduce the use/misuse of antimicrobials and disrupt these multifaceted, interrelated, and interdependent factors are urgently needed. This paper leverages prior research to describe complex major determinants of antimicrobial resistance and provides fresh insights into possible intervention strategies to tackle antimicrobial resistance including in the current and future pandemics.
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Affiliation(s)
- Hyacinth O Ukuhor
- Saudi Electronic University, Department of Public Health, P. O. Box 93499, Riyadh 11673, Saudi Arabia.
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Majumder MAA, Rahman S, Cohall D, Bharatha A, Singh K, Haque M, Gittens-St Hilaire M. Antimicrobial Stewardship: Fighting Antimicrobial Resistance and Protecting Global Public Health. Infect Drug Resist 2020; 13:4713-4738. [PMID: 33402841 PMCID: PMC7778387 DOI: 10.2147/idr.s290835] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious threat to global public health. It increases morbidity and mortality, and is associated with high economic costs due to its health care burden. Infections with multidrug-resistant (MDR) bacteria also have substantial implications on clinical and economic outcomes. Moreover, increased indiscriminate use of antibiotics during the COVID-19 pandemic will heighten bacterial resistance and ultimately lead to more deaths. This review highlights AMR's scale and consequences, the importance, and implications of an antimicrobial stewardship program (ASP) to fight resistance and protect global health. Antimicrobial stewardship (AMS), an organizational or system-wide health-care strategy, is designed to promote, improve, monitor, and evaluate the rational use of antimicrobials to preserve their future effectiveness, along with the promotion and protection of public health. ASP has been very successful in promoting antimicrobials' appropriate use by implementing evidence-based interventions. The "One Health" approach, a holistic and multisectoral approach, is also needed to address AMR's rising threat. AMS practices, principles, and interventions are critical steps towards containing and mitigating AMR. Evidence-based policies must guide the "One Health" approach, vaccination protocols, health professionals' education, and the public's awareness about AMR.
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Affiliation(s)
- Md Anwarul Azim Majumder
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Sayeeda Rahman
- School of Medicine, American University of Integrative Sciences, Bridgetown, Barbados
| | - Damian Cohall
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Ambadasu Bharatha
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Keerti Singh
- Faculty of Medical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | - Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan, Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, Malaysia
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Carretero O, Rivas G, Loras C, Orellana MA. Rapid identification of bacteria directly from positive blood cultures by a modified method using a serum separator tube and matrix-assisted laser desorption ionization – time of flight MS. J Med Microbiol 2020; 69:1373-1380. [DOI: 10.1099/jmm.0.001270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Introduction. Several studies have used matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF) with a serum separator tube (SST) to perform rapid identification of microorganisms directly from positive blood cultures (BCs), with different performances and methodologies.
Hypothesis / Gap Statement. The use of TSS could significantly reduce the time of identification of microorganisms that produce bacteremia.
Aim. Our goals were to evaluate bacterial identification by MALDI-TOF using a method based on an SST and compare it with MALDI-TOF after subculture for 18–24 h.
Methodology. BCs no more than 1 h after a positive growth signal were included in the study. Analysis of results was expressed as a score. Information about time to a positive signal and number of microorganisms was collected.
Results. In total, 253 BCs were analysed; 45.5 % gave a reliable result, 23.3 % an unreliable result and 31.2 % an error in identification. In gram-negative and gram-positive bacteria, the percentages of reliable results were 83.5 and 21.8 %, respectively. According to time to positive signal, the percentages of correct identification and mean score were 81.1 % (99/122) and 1.89±0.30 in Group 1 (<15 h); and 57.2 % (75/131) and 1.70±0.32 in Group 2 (>15 h), respectively (P <0.001). According to the number of microorganisms, the corresponding percentages of correct identification and mean scores were: Group 1 [≤50 microorganisms observed per field (MOF)], 50/94 (53.19 %) and 1.72±0.32; Group 2 (51–100 MOF): 44/66 (66.67 %) and 1.85±0.34; Group 3 (>100 MOF): 79/93 (84.94 %) and 1.84±0.31.
Conclusion. This method allowed us to obtain a high percentage of the aetiological agent of bacteraemia in less than 30 min after a positive BC.
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Affiliation(s)
- Octavio Carretero
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Gonzalo Rivas
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Cristina Loras
- Department of Microbiology, Hospital Universitario de Getafe, Madrid, Spain
| | - M. Angeles Orellana
- Department of Microbiology, Hospital Universitario 12 de Octubre, Madrid, Spain
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Berneking L, Both A, Berinson B, Hoffmann A, Lütgehetmann M, Aepfelbacher M, Rohde H. Performance of the BD Phoenix CPO detect assay for detection and classification of carbapenemase-producing organisms. Eur J Clin Microbiol Infect Dis 2020; 40:979-985. [PMID: 33245470 PMCID: PMC8084821 DOI: 10.1007/s10096-020-04094-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/28/2020] [Indexed: 02/08/2023]
Abstract
Increasing worldwide, prevalence of carbapenem-resistant gram-negative bacteria demands urgent a need for rapid detection and accurate identification of carbapenemases. The BD Phoenix CPO detect (PCD) assay possesses an in-built capacity for parallel susceptibility testing and detection of carbapenemases. Here, the ability of the assay to detect and classify carbapenemase production was tested in a collection of carbapenem-resistant Enterobacterales and non-fermentative gram-negative rods. The ability of the PCD assay to detect and classify carbapenemases was investigated in a collection of 194 clinical, carbapenem-resistant isolates (Enterobacterales [n = 65]; non-fermentative gram-negative rods [n = 129]). AST results were compared to MICS determined by gradient diffusion to determine accuracy of the PCD assay. The accuracy of the PCD assay to detect carbapenemases was compared to the results of molecular isolate characterization using a LDT multiplex carbapenemase PCR assay. All 194 isolates classified as carbapenem-resistant by reference susceptibility testing were also classified correctly as CRO by the PCD assay. Performance analysis of the PCD assay to detect carbapenemase production revealed an overall sensitivity of 98.29% and specificity of 17.95% for the detection of carbapenemase production. For the classification of carbapenemases classes A, B, and D, the PCD correctly classified 79.17% Enterobacterales and 67.16% non-fermentative gram-negative rods. The PCD assay is a reliable tool for the detection of carbapenem resistance and allows for parallel analysis of carbapenemase production. However, while sensitivity is high, low specificity in carbapenemase detection and erroneous classification demands mandatory confirmation by alternative methods, especially in non-fermentative gram-negative bacteria.
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Affiliation(s)
- Laura Berneking
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany
| | - Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany
| | - Benjamin Berinson
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany
| | - Armin Hoffmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany
| | - Marc Lütgehetmann
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Universitätsklinikum Hamburg-Eppendorf, Martinistraße 52, D-20246, Hamburg, Germany.
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Briggs N, Campbell S, Gupta S. Advances in rapid diagnostics for bloodstream infections. Diagn Microbiol Infect Dis 2020; 99:115219. [PMID: 33059201 DOI: 10.1016/j.diagmicrobio.2020.115219] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/12/2020] [Accepted: 09/12/2020] [Indexed: 10/23/2022]
Abstract
Septicemia from bloodstream infections (BSI) is the second largest cause of inpatient mortality and the single most expensive condition for US hospitals to manage. There has been an explosive development of commercial diagnostic systems to accelerate the identification and antimicrobial susceptibility testing (AST) of causative pathogens. Despite adoption of advanced technologies like matrix-assisted laser desorption imaging-time-of-flight mass spectrometry and multiplex polymerase chain reaction for rapid identification, clinical impact has been variable, in part due to the persistent need for conventional AST as well as prescriber understanding of these rapidly evolving platforms. Newer technologies are expanding on rapid detection of genotypic determinants of resistance, but only recently has rapid phenotypic AST been available. Yet, improved outcomes with rapid diagnostic platforms are still most evident in conjunction with active antimicrobial stewardship. This review will outline key advancements in rapid diagnostics for BSI and the role of antimicrobial stewardship in this new era.
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Affiliation(s)
- Neima Briggs
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Sheldon Campbell
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT
| | - Shaili Gupta
- Department of Medicine, Yale School of Medicine, New Haven, CT; Department of Medicine, Division of Infectious Diseases, VA Healthcare Systems of CT, West Haven, CT.
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48
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Martins A, Wink P, Pereira D, Souza A, Aquino V, Barth A. Rapid antimicrobial susceptibility of Enterobacteriaceae by disk diffusion directly from blood culture bottles using the EUCAST RAST breakpoints. J Glob Antimicrob Resist 2020; 22:637-642. [DOI: 10.1016/j.jgar.2020.05.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/22/2020] [Accepted: 05/28/2020] [Indexed: 01/16/2023] Open
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Pharmacist-Driven Implementation of Fast Identification and Antimicrobial Susceptibility Testing Improves Outcomes for Patients with Gram-Negative Bacteremia and Candidemia. Antimicrob Agents Chemother 2020; 64:AAC.00578-20. [PMID: 32601164 PMCID: PMC7449197 DOI: 10.1128/aac.00578-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Bloodstream infections (BSI) are associated with increased morbidity and mortality, especially when caused by Gram-negative or fungal pathogens. The objective of this study was to assess the impact of fast identification-antimicrobial susceptibility testing (ID/AST) with the Accelerate Pheno system (AXDX) from May 2018 to December 2018 on antibiotic therapy and patient outcomes. A pre-post quasiexperimental study of 200 patients (100 pre-AXDX implementation and 100 post-AXDX implementation) was conducted. Bloodstream infections (BSI) are associated with increased morbidity and mortality, especially when caused by Gram-negative or fungal pathogens. The objective of this study was to assess the impact of fast identification-antimicrobial susceptibility testing (ID/AST) with the Accelerate Pheno system (AXDX) from May 2018 to December 2018 on antibiotic therapy and patient outcomes. A pre-post quasiexperimental study of 200 patients (100 pre-AXDX implementation and 100 post-AXDX implementation) was conducted. The primary endpoints measured were time to first antibiotic intervention, time to most targeted antibiotic therapy, and 14-day hospital mortality. Secondary endpoints included hospital and intensive care unit (ICU) length of stay (LOS), antibiotic intensity score at 96 h, and 30-day readmission rates. Of 100 patients with Gram-negative bacteremia or candidemia in each cohort, 84 in the preimplementation group and 89 in the AXDX group met all inclusion criteria. The AXDX group had a decreased time to first antibiotic intervention (26.3 versus 8.0, P = 0.003), hours to most targeted therapy (14.4 versus 9, P = 0.03), hospital LOS (6 versus 8, P = 0.002), and average antibiotic intensity score at 96 h (16 versus 12, P = 0.002). Both groups had a comparable 14-day mortality (0% versus 3.6%, P = 0.11). In this analysis of patients with Gram-negative bacteremia or candidemia, fast ID/AST implementation was associated with decreased hospital LOS, decreased use of broad-spectrum antibiotics, shortened time to targeted therapy, and an improved utilization of antibiotics within the first 96 h of therapy.
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50
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Pilmis B, Thy M, Diep J, Krob S, Périllaud C, Couzigou C, Vidal B, Mizrahi A, Lourtet-Hascoët J, Le Monnier A, Nguyen Van JC. Clinical impact of rapid susceptibility testing on MHR-SIR directly from blood cultures. J Antimicrob Chemother 2020; 74:3063-3068. [PMID: 31377768 DOI: 10.1093/jac/dkz271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND In a previous study, we demonstrated that rapid antibiotic susceptibility tests (ASTs) can be performed directly on blood culture samples tested on Mueller-Hinton Rapid agar (MHR-SIR) with a time delay of 6-8 h. OBJECTIVES Using this rapid disc diffusion method, we analysed the clinical impact associated with rapid reporting of results in our hospital setting. METHODS All patients with bloodstream infections (BSIs) related to Enterobacteriaceae or Staphylococcus aureus were prospectively included in the study. The rapid ASTs were performed by incubation of positive blood cultures on MHR-SIR for 6-8 h by direct inoculation according to BSAC recommendations. RESULTS One hundred and sixty-seven patients with BSIs were included as MHR-guided adaptation therapy cases. Eighty percent had Enterobacteriaceae-related BSIs, of which 12 (9%) were ESBL producers and 20% were S. aureus-related BSIs. A urinary or intra-abdominal infection was observed in 44.3% and 19.8%, respectively, of Enterobacteriaceae-related infections. The most frequent sources of infections for S. aureus BSIs were cutaneous and endovascular, in 43% and 23% of cases, respectively. Forty-four percent of the patients benefited from therapeutic modification according to the results of the MHR-SIR AST. Thus, empirical antibiotic therapy was modified by using antibiotic therapy that had too wide a spectrum or was unsuitable in 26% and 18% of cases, respectively. Compared with the 24 h required for the reference method, the median length of time to provision of susceptibility test results by MHR-SIR was 7 h. CONCLUSIONS This study showed a significant time saving (17 h) on the appropriateness of antibiotic prescription and demonstrated a significant impact regarding the choice and reduction of the spectrum of antibiotic therapy.
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Affiliation(s)
- Benoît Pilmis
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Michael Thy
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Julien Diep
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Sophie Krob
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Claire Périllaud
- Service de microbiologie clinique et dosage des anti-infectieux, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Carine Couzigou
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France.,Equipe opérationnelle d'hygiène, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Barbara Vidal
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France.,Equipe opérationnelle d'hygiène, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Assaf Mizrahi
- Service de microbiologie clinique et dosage des anti-infectieux, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Julie Lourtet-Hascoët
- Equipe mobile de microbiologie clinique, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Alban Le Monnier
- Service de microbiologie clinique et dosage des anti-infectieux, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
| | - Jean-Claude Nguyen Van
- Service de microbiologie clinique et dosage des anti-infectieux, Groupe Hospitalier Paris Saint-Joseph, 75014 Paris, France
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